I. AA SEPARATION – gel electrophoresis

1. Gel electrophoresis – separates AAs based on their charge; AAs are put into a gel then exposed to the electric field; the AAs will migrate through the get based on their charge and external electric field

2. Think about this: when pH < pI, that means there are lots of H+s floating around and some are bound to attach to the AA, making the net charges more (+), more attracted to the (-) electrode

3. When pH > pI, that means there are few H+s floating around, so more will be pulled off the AA, making the net charge more (-), and more attracted to (+) electrode

II. 8.2: PROTEINS

AAs hooked together by peptide bonds or disulfide bridges (only between cysteine R-groups)

A. THE PEPTIDE BOND

1. Between carboxyl group of one AA and the α-amino group of another AA through hydrolysis

2. Peptide = amide (N–C=O)

3. Not thermodynamically favorable; requires energy

B. DCC COUPLING

1. Used to artificially synthesize peptides in labs

2. Pattern of backbone is N–C–C–N–C–C

3. In naming, 1st AA named is the amino terminus; last one named is the carboxy terminus AA

4. Residue – AAs in peptides are referred to as residues

C. PLANARITY OF THE PEPTIDE BOND

1. No rotation around a peptide bond because of double-bond character between carbonyl C and N

2. This results in a rigid, planar structure

D. HYDROLYSIS OF THE PEPTIDE BOND

1. Thermodynamically favored (see image above), but kinetically slow

2. Can be sped up with:

a) Strong acids (and heat)

b) Proteolytic enzymes (protease); many cleave bonds at specific AAs

E. THE DISULFIDE BOND

Only formed between R groups of 2 cysteine AA side groups

1. Important in stabilizing tertiary protein structure

2. Cysteine–cysteine → becomes cystine when bound together

F. PROTEIN STRUCTURE IN 3D

1. Primary Structure: The AA sequence

a) Referred to as sequence

b) Peptide bond determines sequence

2. Secondary Structure: Hydrogen bonds between backbone groups

a) Refers to initial folding of a polypeptide chain into shapes stabilized by H-bonds (between N-H and C-O groups)

b) α-helixes

(1) Formed by backbone spiral where H-bonding occurs between residues in the same chain that line up in the coil (N-H and C-O groups)

(2) Proline never appears within α-helix

(3) α-helixes are used in transmembrane proteins; all the partially charged areas are interacting with each other, and ∴ don’t interact with the hydrophobic membrane

c) β-pleated sheets

(1) β-pleated sheets have H-bonding between N-H and C-O groups, but they are often on separate chains

(2) Backbone is stretched out with side groups above and below the side chains

3. Tertiary Structure: Hydrophobic/Hydrophilic Interactions

a) Further folding of the secondary structure; usually driven by R-groups and their interactions with the solvent

b) H-bonding and hydrophobic interactions often cause a protein to spontaneously fold into the correct conformation

c) Orthophosphate has ↑ favorable interaction with water than linked phosphates

B. NUCLEOTIDES

1. ATP – used in cellular metabolism in addition to being RNA precursor

CHAPTER 8 SUMMARY:

○ AAs consist of tetrahedral α-C connected to an amino group, a carboxyl group, and a variable R group which determines AA’s properties

○ The isoelectric point of an AA is the pH at which the net charge on the molecule is zero; this structure is referred to as the zwitterion

○ Electrophoresis separates mixtures of AAs and is contuced at buffered pH; (+) AAs move to the (-) end of the gel, and (-) AAs move to the (+) end’Proteins consist of AAs linked by peptide bonds, which have partial ⚌ characteristics, lack rotation, and are very stable

○ The 2° structure of proteins (α-helices and β-sheets) is formed through H-bonding between atoms in the backbone of the molecule

○ The most stable 3° protein structure generally places polar AAs on the exterior and nonpolar AAs on the interior of the protein; this minimizes interactions between nonpolar AAs and sater, while optimizing interactions between side chains inside the protein

○ All animal AAs are L-configuration (amine group in L position) and all animal sugars are D-configuration

○ Carbohydrates are chains of hydrated C atoms with the molecular formula CnH2nOn

○ Sugars in solution exist in ⇋ between the straight chain form and either the furanose or pyranose cyclic forms

○ The anomeric forms of a sugar differ by the position of the OH group on the anomeric C

■ OH- down = α

■ OH- up = β

○ All monosaccharides will give a positive result in a Benedict’s test because they contain an aldehyde, ketone or hemiacetal, and are ∴ reducing sugars

○ The glycosidic linkages in a disaccharide is named based on which anomer is present for the sugar containing the acetal and the number of the C linked to the bridging O